New Beginnings
by HobbitBadger
Summary: An AU with Miranda still serving aboard the Normandy during the Reaper War, causing friction between her and Major Alenko. Primarily Kaidan and Miranda POVs but other characters might wheedle their way in too. As usual Bioware owns Mass Effect.
1. Author's Note

What follows is a brief prologue to the following AU of Mass Effect 3, just to clear up a few points and because I can't resist writing up headcanon.

Following the events of the Suicide Mission, the Collector base was saved but Shepard passed as much information about the Collectors, and the way through the Omega-4 Relay, to the Council rather than surrendering it to Cerberus. After several clashes with Council reconnaissance forces, Cerberus conducted a large raid through the relay, taking the remnants of the proto-Reaper from the Collector Base and disappearing, maintaining an ominous silence ever since.

Shepard cut all ties with Cerberus and, through Councillor Udina's machinations and in recognition of the Collector intel Shepard had acquired, Shepard's Spectre status was officially upheld. Her rank of Staff Commander was reinstated but she is currently on permanent secondment to the Spectre Office.

The _Normandy SR-2_, despite heavy damage during the Suicide Mission and losses amongst the crew, is re-fitted and remains under Shepard's command as "an independent Spectre vessel". After a full refit (funded from Shepard's previously unknown personal resources) _Normandy_ is frequently seen heading between the homeworlds of all Citadel races with long sojourns in the Terminus.

Doctor Liara T'Soni, as Deputy to the Shadow Broker, established an operations and communications room in the former armoury on the CIC deck.

One Lieutenant James Vega of the Alliance Marine Corps, rescued by Shepard and Garrus Vakarian from a bar brawl on Omega, is attached to the _Normandy_ as an Alliance Military Observer and replaced deceased Jacob Taylor as Armoury Chief and head of the marine detachment.

Chief Engineer Tali'Zorah vas Normandy returned to the Flotilla to delay any moves towards war with the Geth. At Shepard's request, the Alliance transferred Lieutenant Greg Adams to the engineering crew of _Normandy_ as a Technical Observer.

Gunnery Officer Garrus Vakarian, left the Normandy to take up a position as Special Operations Advisor the Primarch of Palaven.

Miranda Lawson, after providing the Spectre Office and Alliance Intelligence, is released on Commander Shepard's authority and resumed her duties as _Normandy_'s Executive Officer. Her release, and service aboard the _Normandy_, is not widely known outside of the Council and Alliance High Command.

The sacrifices made by Jacob Taylor, Zaeed Massani and Justicar Samara, ands those who died during the service the _Normandy SR-1_ are recognised on the SR-2's memorial wall located on the crew deck.

In the six months between the _Normandy_'s assault on the Collector Base and the beginning of the Reaper War, there was a catastrophic disaster deep within Batarian space when the Alpha Relay mysteriously exploded and took the Bahak system with it. Although the events around the annihilation of Bahak remain shrouded in mystery, The Batarian Hegemony made accusations about Alliance interference in the system prior to the relay's explosion and that a vessel bearing a strong similarity to the _Normandy_ was recorded by Hegemony surveillance stations heading through Batarian space at the same time. Commander Shepard denied any involvement with the Bahak disaster but voluntarily submitted herself before an joint Council-Alliance investigation on Earth in 2186.


	2. Memories and Reunions

He couldn't tear his eyes away from the city. _Vancouver's burning. My home is burning. Dear God keep Mom and Dad safe. _

He felt a hand rest softly on his shoulder."Come on Kaidan, we've got to go. We need to get to Mars." The gentleness in her voice was at odds with her normal clipped formality.

He closed his eyes and turned away from the view being eclipsed by the elevating ramp. "Yeah, you're right. We need to go." When he opened his eyes, Shepard was already striding for the elevator.

"So we're running away? Just like that?" Kaidan glanced over at the burly lieutenant, Vega, his voice choking with indignation.

Shepard stopped mid-stride and glanced over he shoulder. "You heard the Admiral, Vega. We can't win this on our own. We're collecting Liara from Mars and then we're getting out of here before the Reapers close off Charon completely."

Vega's face darkened. "Since when did you start blindly obeying orders _Commander_?" The sneer in his voice got Alenko's hackles up; Vega seemed a decent sort but his attitude was going to start causing trouble fast. He opened his to call the younger man up but Shepard got there first.

She turned back towards Kaidan and Vega, meeting the lieutenant's glare with her own cool, even stare. "The same day you replaced your brains with varren crap marine." Kaidan remembered that tone well; the calm, collected voice that only just masked the temper beneath it. "This is just one ship, and no matter good she is or how good her crew is that means damn-all against several hundred Reapers." She began walking slowly towards Vega under until she was having to stare up at him. "We need _all_ the fleets in the galaxy combined to stand a chance." She curled her lip. "So swallow your damn pride, and keep that anger for the Reapers, not me. Get your gear ready for Mars." Without waiting for a response she turned back to the elevator.

Vega looked at Kaidan, seeking support but all he could do was shrug. "The Commander's right Lieutenant. You know it, I know it, and that doesn't make it easier. But you better learn to deal with it. Fast." And he followed Shepard towards the elevator. Before the doors closed, he looked back; Vega was rooted the spot but the anger had been replaced by bleakness.

"Thanks for the support Major." Kaidan glanced side-long at the woman standing beside him. Out of Vega's sight, in this isolated box, her shoulders slumped and an emotion flickered across her face he hadn't seen in years; sorrow. _Not since Virmire. _Mentally he forced down the image of a lean, tanned marine, dark hair framing a face alight with mischief. _Not now, I really don't need this now. Focus on the task in hand. _

"No problem Commander, just doing my job." Shepard flinched imperceptibly, and Kaidan felt a sinking feeling in his guts. _A brilliant choice of words Major._ He changed topic quickly. "So why is Liara on Mars?"

Shepard straightened herself noticeably, the cool composure of the Commander falling into place again. "She believes there's something buried deep in the Archives. Something that can help us against the Reapers."

Kaidan raised his eyebrows and was about to ask more when the doors slid open and they were in _Normandy_'s CIC.

For a brief moment, Kaidan was thrown off by a feeling of familiarity, recalling the hours he'd spent here. Going over the campaign in the conference room. Liaising with Pressly about duty rosters. Blithely ignoring Joker's attempts to make digs about him and Ash. But then he came back to reality with a sickening drop. _This isn't Normandy. This an enlarged reproduction. Ash is gone. Pressly's gone_.

And somebody else was standing in Pressly's usual spot by the galaxy map. A tall woman with raven-black hair in an figure-hugging catsuit with an aura of professionalism that put Shepard's in the shade. Alenko frowned, recognition of the woman sinking in. _Her again_.

Shepard had already walked up to the podium over the galaxy map. "Miranda, what's our status?" She asked, leaning on the railing as the dark-haired moved up beside her, a datapad in hand.

"We're ten minutes out of Mars, Commander. Stealth systems are ready to come online as soon as we drop out of FTL. EDI hasn't detected any Reapers presence on the surface but we'd better be quick all the same." There was the hint of an Australian accent, just as he remembered. _Minus the sneer it held on Horizon._

"And the shuttle?"

The woman nodded. "Already being prepped. We picked up a shuttle pilot during the quick evac from Vancouver so I got him to work on the shuttle straight away." She looked down briefly at pad in her hand as it pinged. "Lieutenant Vega has just reported in, he's giving the pilot a hand getting the shuttle ready and gear stowed."

"At least he's got his act together." Shepard muttered. She paused, noticing Kaidan still in the doorway of the elevator, frowning at Miranda. "Kaidan Alenko, Miranda Lawson, _Normandy_'s XO." Nodding her head towards Kaidan, "Miranda Lawson, Major Kaidan Alenko of Biotics Division."

Miranda gave a tight-lipped smile to Kaidan. "Major, I'm sorry we have to meet in these circumstances."

Alenko kept frowning. "You think they'd be more cordial in different circumstances?" His voice sounding overly harsh to his own ears. _What is __**she**__ doing as Normandy's XO? _Kaidan looked towards Shepard, who was now frowning at him. _What the hell are you doing Shepard? Why is Cerberus still on this ship?_

The woman, _Miranda_, arched an eyebrow. "Is there a problem Major?" Kaidan suppressed to urge to laugh, knowing how bitter it would sound. _Commander Shepard is supposed to have left Cerberus behind? The Normandy is "an independent Spectre vessel" and I find one of Cerberus' top officers serving onboard? Why should there be a problem?_

"That depends Executive Lawson." He was trying to keep his tone even, and failing. "The last time I checked you were working for Cerberus." He stared at her, long and hard.

Executive Lawson stared right back, her expression cool."You should conduct your checks more frequently Major."

Then Shepard between them. "Enough, both of you, we've got more important things at hand right now. Like a Reaper invasion" She looked at her XO. "Do we have any spare armour for the Major?"

Lawson flicked her gaze away from Kaidan to Shepard. "Of course Commander, I'll inform Lieutenant Vega to have a set ready and weapons for Major Alenko's selection.." A chilly note entering the Australian lilt.

Shepard nodded. "Very well, I'll collect my gear. You have the deck Miranda." She stepped down from the podium, looking towards Kaidan, her eyes alight with annoyance. "Kaidan, with me." And they stepped back into the elevator. Once the doors closed she pivoted on her heel, her deep blue eyes narrowed. "I can guess what you're thinking but _please_ leave it alone until we've got Liara out of the Archives. Vega's already on a short fuse and I can't afford to be keeping a watch over both of you."

Kaidan gave her a long, searching look. _As though "Cerberus" is going to be written in capital letters on her forehead. _"Sorry ma'am, but what I supposed to think? You claim you've quit Cerberus, that you've returned to the Alliance but you have the Illusive Man's protégé as your second-in-command?" He swallowed hard. "After all Cerberus did for you, after all they _did to you _I'm supposed to take your word you've broken all ties just like that? With _Miranda Lawson_ directing your CIC?"

But Shepard didn't look away. _She always stands by her choices, even the bad ones, with no regrets. She told me that herself._ "Miranda left Cerberus with me Kaidan. She left because she trusted _me_ more than the Illusive Man. I'd be an idiot if I cut someone with her talents adrift." Then her shoulders slumped ever so slightly, rubbing her forehead with the palm of her hand. "Please, just trust me on this. I've cut all ties to Cerberus and so has Miranda. All of us need to work together on this, otherwise we're all sunk and the Reapers will turn Earth, Palaven, Thessia and dozens of other worlds into slag."

The elevator pinged as the doors opened again. "This my stop Major, I'll see you in the cargo bay, geared up and ready, in five. We've got a Prothean expert with a secret weapon to evacuate."

He sighed. "Yes Commander." And then she was gone, and the elevator doors closed again.

On the way down, Kaidan's head was whirling with thoughts. _Shepard may have left Cerberus. She's done some dark things but she's no human supremacist. But Lawson? The woman who's been with Cerberus for fifteen years, and is so high up the chain not even the Broker could get to her, suddenly has a change of heart?_

Kaidan took several deep breaths, trying to calm himself. _ Trust Shepard? After all we've been through together she deserves that much,especially after that fiasco back on Horizon. But trust Lawson? The one who disdained him as a blind Alliance fool when she worked for a twisted group like Cerberus? Not even if St Peter came down and told me to give her chance._

He shook his head ruefully. _Ash has a lot to answer for. I wish you were here to haul my ass out of the fire__ like old times Chief._

The doors opened on the cargo bay. _If nothing else you were easier on the eyes than Lieutenant Vega._ He could almost hear that irreverent cackle coming from the armoury station.

* * *

**A/N This is something that's been knocking about in my head for a while so I thought I'd try and put some of it into words. As always, constructive criticism gratefully received!**


End file.
